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Author	SHA1	Message	Date
James Fellows Yates	cc73cdd51d	Add generation of taxon-table like output for MALT	2022-04-16 07:42:30 +02:00
James A. Fellows Yates	6fecb3eeb7	Merge pull request #54 from nf-core/dev ... Get upstream changes	2022-04-16 06:17:33 +02:00
sofstam	0e5c9e7bdd	Type:boolean for kaiju in nextflow_schema.json	2022-04-14 09:14:05 +02:00
sofstam	6736a2a980	Update README.md, nextflow_schema.json	2022-04-13 19:00:52 +02:00
sofstam	68ce5843a4	Add kaiju in taxprofiler	2022-04-13 18:51:56 +02:00
James A. Fellows Yates	fc8a83245a	Add short-read host removal via BowTie2 alignment mapping ... Add short-read host removal via BowTie2 alignment mapping	2022-04-13 15:29:16 +02:00
James A. Fellows Yates	5e80df0f94	Apply suggestions from code review	2022-04-13 15:27:53 +02:00
James Fellows Yates	aa2d07c42a	Fix merge cockup	2022-04-13 14:19:19 +02:00
James A. Fellows Yates	70f94603b0	Merge branch 'dev' into hostremoval	2022-04-13 13:59:51 +02:00
James A. Fellows Yates	67d94a9a8d	Merge pull request #45 from nf-core/run-merging ... Re-add run merging	2022-04-13 12:27:37 +02:00
James Fellows Yates	dfeaa0d1fe	Rename subworkflow parameters for consistency	2022-04-13 12:00:28 +02:00
James Fellows Yates	de57340526	Start work	2022-04-13 11:49:35 +02:00
James Fellows Yates	16a3556bfc	Changes after code review	2022-04-13 08:26:08 +02:00
James Fellows Yates	a15c45b00c	Put map in the rigt place	2022-04-12 10:51:27 +02:00
James Fellows Yates	8d68914192	Re-add operator name	2022-04-12 10:47:44 +02:00
James Fellows Yates	26399718b2	Re-add pairment attachment	2022-04-12 10:46:03 +02:00
James Fellows Yates	2ef21c6ef3	Fix input to profiling	2022-04-12 10:14:05 +02:00
James Fellows Yates	9f221f84cc	Only supply single input channel to profiling, as these are merged into single input channel at run_merging	2022-04-12 10:12:17 +02:00
James A. Fellows Yates	967b1f7d6e	Merge branch 'dev' into run-merging	2022-04-12 09:28:10 +02:00
James Fellows Yates	a5f4fc42d5	Fix run merging for unmerged PE data	2022-04-12 09:25:27 +02:00
James A. Fellows Yates	1ac5a129a8	Merge pull request #52 from genomic-medicine-sweden/delete_extra_directory ... Delete extra unnecessary directory	2022-04-11 20:46:50 +02:00
sofstam	989dc55ce1	Delete extra nf-core directory	2022-04-11 17:42:38 +02:00
James Fellows Yates	78182c2a8c	Add comma	2022-04-11 13:40:24 +02:00
James Fellows Yates	ff2e508a38	Merge branch 'hostremoval' of github.com:nf-core/taxprofiler into hostremoval	2022-04-11 13:38:53 +02:00
James Fellows Yates	29073e3c93	Update CI tests	2022-04-11 13:38:42 +02:00
James A. Fellows Yates	025083061e	Merge branch 'dev' into hostremoval	2022-04-11 13:36:03 +02:00
James A. Fellows Yates	fb2f5ed73e	Merge pull request #50 from nf-core/docs-prelim ... Initial attempt at adding usage docs	2022-04-11 10:52:18 +02:00
James A. Fellows Yates	b8b11fd065	Apply suggestions from code review ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-04-11 10:30:29 +02:00
James Fellows Yates	b892fd0be5	Initial attempt at docs	2022-04-10 22:17:44 +02:00
James A. Fellows Yates	dd22e042be	Merge pull request #47 from nf-core/profiling-subworkflow ... Move profiling to subworkflow	2022-04-10 16:54:35 +02:00
James Fellows Yates	030099c559	A bit of clean up	2022-04-10 07:26:20 +02:00
James Fellows Yates	80c08af11b	Mix in profiling versions into mainline versons channel	2022-04-10 06:48:25 +02:00
James Fellows Yates	082093f3de	Prettier	2022-04-10 06:44:10 +02:00
James Fellows Yates	ecf0eea4f9	Move profiling to subworkflow and standardise outputs	2022-04-10 06:43:30 +02:00
James Fellows Yates	afb66e445f	Append pairment to ID at profiling to prevent multiqc-level filename crash	2022-04-08 21:36:59 +02:00
James Fellows Yates	8839fe22b8	Fix output tuple for reads	2022-04-08 20:02:22 +02:00
James Fellows Yates	35cb6e042a	Flatten the right thing	2022-04-08 13:46:12 +02:00
James Fellows Yates	6c14f2b230	Remove the flattening?	2022-04-08 13:44:52 +02:00
James Fellows Yates	a634814d84	Formatting and fix fastp output	2022-04-08 13:34:00 +02:00
James Fellows Yates	ca011ccc5b	Fix cat_fastq naming logic?	2022-04-08 13:28:37 +02:00
James Fellows Yates	d130a72d74	Get this working	2022-04-08 13:09:23 +02:00
James Fellows Yates	4d726a87e9	Fix metadata removal	2022-04-08 12:01:07 +02:00
James Fellows Yates	74c496f6af	Fix CAT_FASTQ output	2022-04-08 11:58:16 +02:00
James Fellows Yates	7b08c49cd6	Re-add run merging and gonna let GHA see if it works >.>	2022-04-08 11:54:54 +02:00
Sofia Stamouli	5f24f94391	Merge pull request #31 from genomic-medicine-sweden/classification_centrifuge ... Add centrifuge classification (centrifuge/centrifuge module)	2022-04-08 11:26:57 +02:00
Sofia Stamouli	63bc597daf	Prettier	2022-04-08 11:01:45 +02:00
Sofia Stamouli	fd5ebea9a6	Remove old centrifuge module	2022-04-08 10:57:58 +02:00
Sofia Stamouli	48d28cf8d4	Update conf/test.config ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-04-08 10:00:10 +02:00
Sofia Stamouli	2dfe3b3cc1	Update conf/test.config ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-04-08 10:00:04 +02:00
Sofia Stamouli	3d45ac57ae	Prettier	2022-04-07 16:42:22 +02:00